flash1dkmeans 0.0.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- flash1dkmeans-0.0.1/.gitignore +160 -0
- flash1dkmeans-0.0.1/.idea/.gitignore +8 -0
- flash1dkmeans-0.0.1/.idea/flash1dkmeans.iml +15 -0
- flash1dkmeans-0.0.1/.idea/inspectionProfiles/Project_Default.xml +15 -0
- flash1dkmeans-0.0.1/.idea/inspectionProfiles/profiles_settings.xml +6 -0
- flash1dkmeans-0.0.1/.idea/misc.xml +7 -0
- flash1dkmeans-0.0.1/.idea/modules.xml +8 -0
- flash1dkmeans-0.0.1/.idea/vcs.xml +6 -0
- flash1dkmeans-0.0.1/.idea/workspace.xml +151 -0
- flash1dkmeans-0.0.1/LICENSE +21 -0
- flash1dkmeans-0.0.1/PKG-INFO +128 -0
- flash1dkmeans-0.0.1/README.md +112 -0
- flash1dkmeans-0.0.1/pyproject.toml +27 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/__init__.py +1 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/config.py +9 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/k_cluster.py +341 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/main.py +300 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/two_cluster.py +157 -0
- flash1dkmeans-0.0.1/src/flash1dkmeans/utils.py +37 -0
- flash1dkmeans-0.0.1/tests/k_cluster.py +9 -0
- flash1dkmeans-0.0.1/tests/two_cluster.py +9 -0
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MIT License
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Copyright (c) 2024 Jake Hyun
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in the Software without restriction, including without limitation the rights
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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copies or substantial portions of the Software.
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.3
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Name: flash1dkmeans
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Version: 0.0.1
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Summary: An optimized K-means implementation for the one-dimensional case.
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Project-URL: Homepage, https://github.com/SyphonArch/flash1dkmeans
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Project-URL: Issues, https://github.com/SyphonArch/flash1dkmeans/issues
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Author-email: Jake Hyun <jake.hyun@hotmail.com>
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License-File: LICENSE
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.8
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Requires-Dist: numba~=0.59.1
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Requires-Dist: numpy~=1.26.4
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Description-Content-Type: text/markdown
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# flash1dkmeans
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An optimized K-means implementation for the one-dimensional case
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Exploits the fact that one-dimensional data can be sorted.
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Numba acceleration is used, so callers can further use parallelization with Numba's `@njit(parallel=True)`
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if multiple instances of the algorithm are run in parallel.
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## Features
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### Two clusters
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Guaranteed to find the optimal solution for two clusters.
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### K clusters
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Uses the K-means++ initialization algorithm to find the initial centroids.
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Then uses the Lloyd's algorithm to find the final centroids, except with optimizations for the one-dimensional case.
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## Time Complexity
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+
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- **2 clusters**: O(log(n))
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- (+ (O(n) for prefix sum calculation if not provided))
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- **k clusters**: O(k * 2 + log(k) * log(n) + max_iter * log(n) * k)
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(+ (O(n) for prefix sum calculation if not provided))
|
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+
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This is a significant improvement over the standard K-means algorithm, which has a time complexity of O(n * k * max_iter),
|
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even excluding the time complexity of the K-means++ initialization.
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+
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## How fast is it?
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TODO: Comparision with sklearn's KMeans
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## Installation
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```bash
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pip install flash1dkmeans
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```
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## Usage
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### Basic usage
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```python
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from flash1dkmeans import kmeans_1d
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data = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]
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k = 2
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centroids, labels = kmeans_1d(data, k)
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```
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### More Options
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```python
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from flash1dkmeans import kmeans_1d
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import numpy as np
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data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
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weights = np.random.random_sample(data.shape)
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k = 3
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centroids, labels = kmeans_1d(
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data, k,
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sample_weights=weights, # sample weights
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n_local_trials=(2 + int(np.log(k))), # number of local tries
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max_iter=100, # maximum number of iterations
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)
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```
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### Even More Options
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```python
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from flash1dkmeans import kmeans_1d
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import numpy as np
|
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n, k = 1024, 4
|
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# Generate random data
|
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data = np.random.random_sample(n)
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data = np.sort(data)
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# Generate random weights
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weights = np.random.random_sample(data.shape)
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# Calculate prefix sums
|
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weights_prefix_sum = np.cumsum(weights)
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weighted_X_prefix_sum = np.cumsum(data * weights)
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weighted_X_squared_prefix_sum = np.cumsum(data ** 2 * weights)
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middle_idx = n // 2
|
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# Providing prefix sums reduces redundant calculations
|
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|
+
# This is useful when the algorithm is run multiple times on different segments of the data
|
|
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+
for start_idx, stop_idx in [(0, middle_idx), (middle_idx, n)]:
|
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centroids, cluster_borders = kmeans_1d(
|
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+
data, k, # Note how the sample weights are not provided when the prefix sums are provided
|
|
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|
+
n_local_trials=(2 + int(np.log(k))), # number of local tries
|
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|
+
max_iter=100, # maximum number of iterations
|
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return_cluster_borders=True, # return cluster borders instead of labels
|
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weights_prefix_sum=weights_prefix_sum, # prefix sum of the sample weights, leave empty for unwieghted data
|
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weighted_X_prefix_sum=weighted_X_prefix_sum, # prefix sum of the weighted data
|
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weighted_X_squared_prefix_sum=weighted_X_squared_prefix_sum, # prefix sum of the squared weighted data
|
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start_idx=start_idx, # start index of the data
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stop_idx=stop_idx, # stop index of the data
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)
|
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```
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|
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## Notes
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This repository has been created to be used in [Any-Precision-LLM](https://github.com/SNU-ARC/any-precision-llm) project,
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where multiple 1D K-means instances are run in parallel for LLM quantization.
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However the algorithm is general and can be used for any 1D K-means problem.
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# flash1dkmeans
|
|
2
|
+
An optimized K-means implementation for the one-dimensional case
|
|
3
|
+
|
|
4
|
+
Exploits the fact that one-dimensional data can be sorted.
|
|
5
|
+
|
|
6
|
+
Numba acceleration is used, so callers can further use parallelization with Numba's `@njit(parallel=True)`
|
|
7
|
+
if multiple instances of the algorithm are run in parallel.
|
|
8
|
+
|
|
9
|
+
## Features
|
|
10
|
+
|
|
11
|
+
### Two clusters
|
|
12
|
+
|
|
13
|
+
Guaranteed to find the optimal solution for two clusters.
|
|
14
|
+
|
|
15
|
+
### K clusters
|
|
16
|
+
|
|
17
|
+
Uses the K-means++ initialization algorithm to find the initial centroids.
|
|
18
|
+
Then uses the Lloyd's algorithm to find the final centroids, except with optimizations for the one-dimensional case.
|
|
19
|
+
|
|
20
|
+
## Time Complexity
|
|
21
|
+
|
|
22
|
+
- **2 clusters**: O(log(n))
|
|
23
|
+
- (+ (O(n) for prefix sum calculation if not provided))
|
|
24
|
+
- **k clusters**: O(k * 2 + log(k) * log(n) + max_iter * log(n) * k)
|
|
25
|
+
(+ (O(n) for prefix sum calculation if not provided))
|
|
26
|
+
|
|
27
|
+
This is a significant improvement over the standard K-means algorithm, which has a time complexity of O(n * k * max_iter),
|
|
28
|
+
even excluding the time complexity of the K-means++ initialization.
|
|
29
|
+
|
|
30
|
+
## How fast is it?
|
|
31
|
+
|
|
32
|
+
TODO: Comparision with sklearn's KMeans
|
|
33
|
+
|
|
34
|
+
|
|
35
|
+
## Installation
|
|
36
|
+
```bash
|
|
37
|
+
pip install flash1dkmeans
|
|
38
|
+
```
|
|
39
|
+
|
|
40
|
+
## Usage
|
|
41
|
+
|
|
42
|
+
### Basic usage
|
|
43
|
+
```python
|
|
44
|
+
from flash1dkmeans import kmeans_1d
|
|
45
|
+
|
|
46
|
+
data = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]
|
|
47
|
+
k = 2
|
|
48
|
+
|
|
49
|
+
centroids, labels = kmeans_1d(data, k)
|
|
50
|
+
```
|
|
51
|
+
|
|
52
|
+
### More Options
|
|
53
|
+
```python
|
|
54
|
+
from flash1dkmeans import kmeans_1d
|
|
55
|
+
import numpy as np
|
|
56
|
+
|
|
57
|
+
data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
|
|
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|
+
weights = np.random.random_sample(data.shape)
|
|
59
|
+
k = 3
|
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60
|
+
|
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61
|
+
centroids, labels = kmeans_1d(
|
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+
data, k,
|
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63
|
+
sample_weights=weights, # sample weights
|
|
64
|
+
n_local_trials=(2 + int(np.log(k))), # number of local tries
|
|
65
|
+
max_iter=100, # maximum number of iterations
|
|
66
|
+
)
|
|
67
|
+
```
|
|
68
|
+
|
|
69
|
+
### Even More Options
|
|
70
|
+
```python
|
|
71
|
+
from flash1dkmeans import kmeans_1d
|
|
72
|
+
import numpy as np
|
|
73
|
+
|
|
74
|
+
n, k = 1024, 4
|
|
75
|
+
|
|
76
|
+
# Generate random data
|
|
77
|
+
data = np.random.random_sample(n)
|
|
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|
+
data = np.sort(data)
|
|
79
|
+
|
|
80
|
+
# Generate random weights
|
|
81
|
+
weights = np.random.random_sample(data.shape)
|
|
82
|
+
|
|
83
|
+
# Calculate prefix sums
|
|
84
|
+
weights_prefix_sum = np.cumsum(weights)
|
|
85
|
+
weighted_X_prefix_sum = np.cumsum(data * weights)
|
|
86
|
+
weighted_X_squared_prefix_sum = np.cumsum(data ** 2 * weights)
|
|
87
|
+
|
|
88
|
+
middle_idx = n // 2
|
|
89
|
+
|
|
90
|
+
# Providing prefix sums reduces redundant calculations
|
|
91
|
+
# This is useful when the algorithm is run multiple times on different segments of the data
|
|
92
|
+
for start_idx, stop_idx in [(0, middle_idx), (middle_idx, n)]:
|
|
93
|
+
centroids, cluster_borders = kmeans_1d(
|
|
94
|
+
data, k, # Note how the sample weights are not provided when the prefix sums are provided
|
|
95
|
+
n_local_trials=(2 + int(np.log(k))), # number of local tries
|
|
96
|
+
max_iter=100, # maximum number of iterations
|
|
97
|
+
return_cluster_borders=True, # return cluster borders instead of labels
|
|
98
|
+
weights_prefix_sum=weights_prefix_sum, # prefix sum of the sample weights, leave empty for unwieghted data
|
|
99
|
+
weighted_X_prefix_sum=weighted_X_prefix_sum, # prefix sum of the weighted data
|
|
100
|
+
weighted_X_squared_prefix_sum=weighted_X_squared_prefix_sum, # prefix sum of the squared weighted data
|
|
101
|
+
start_idx=start_idx, # start index of the data
|
|
102
|
+
stop_idx=stop_idx, # stop index of the data
|
|
103
|
+
)
|
|
104
|
+
```
|
|
105
|
+
|
|
106
|
+
## Notes
|
|
107
|
+
|
|
108
|
+
This repository has been created to be used in [Any-Precision-LLM](https://github.com/SNU-ARC/any-precision-llm) project,
|
|
109
|
+
where multiple 1D K-means instances are run in parallel for LLM quantization.
|
|
110
|
+
|
|
111
|
+
However the algorithm is general and can be used for any 1D K-means problem.
|
|
112
|
+
|
|
@@ -0,0 +1,27 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["hatchling"]
|
|
3
|
+
build-backend = "hatchling.build"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "flash1dkmeans"
|
|
7
|
+
version = "0.0.1"
|
|
8
|
+
authors = [
|
|
9
|
+
{ name="Jake Hyun", email="jake.hyun@hotmail.com" },
|
|
10
|
+
]
|
|
11
|
+
description = "An optimized K-means implementation for the one-dimensional case."
|
|
12
|
+
readme = "README.md"
|
|
13
|
+
requires-python = ">=3.8"
|
|
14
|
+
classifiers = [
|
|
15
|
+
"Programming Language :: Python :: 3",
|
|
16
|
+
"License :: OSI Approved :: MIT License",
|
|
17
|
+
"Operating System :: OS Independent",
|
|
18
|
+
]
|
|
19
|
+
dependencies = [
|
|
20
|
+
"numba~=0.59.1",
|
|
21
|
+
"numpy~=1.26.4"
|
|
22
|
+
]
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
[project.urls]
|
|
26
|
+
Homepage = "https://github.com/SyphonArch/flash1dkmeans"
|
|
27
|
+
Issues = "https://github.com/SyphonArch/flash1dkmeans/issues"
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
from .main import kmeans_1d
|